---
title: "Fastp"
author: "Pierre Barry"
date: "`r format(Sys.time(), '%d %B, %Y, %H:%M')`"
output:
flexdashboard::flex_dashboard:
theme: paper
orientation: rows
social: menu
source_code: embed
vertical_layout: scroll
---
```{r global, include=FALSE}
PRINT_IMAGE = 0
list.of.packages <- c("RColorBrewer","DT","ggplot2","png","plotly")
for (i in list.of.packages){
if (i %in% installed.packages()[,"Package"] == FALSE){
install.packages(i)
}
eval(bquote(library(.(i))))
}
```
```{r, include = FALSE}
color_med_atl=data.frame(Location=c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
Col=brewer.pal(n = 4, name = "RdBu"))
```
Fastp {data-icon="fa-laptop"}
=======================================================================
```{r}
fastp_process<-read.table(paste(path,"/data/fastp/Summary_fastp.txt",sep = ""),sep=";",header=F)
colnames(fastp_process)=c("SAMPLE",
"TOTAL_READS_BEFORE_FILTERING","TOTAL_BASES_BEFORE_FILTERING",
"GC_CONTENT_BEFORE_FILTERING","Q20_RATE_BEFORE_FILTERING",
"Q30_RATE_BEFORE_FILTERING","PASSED_FILTER_READS","CORRECTED_READS","CORRECTED_BASES",
"LOW_QUALITY_READS","TOO_MANY_N_READS","TOO_SHORT_READS","LOW_COMPLEXITY_READS",
"TOTAL_READS_AFTER_FILTERING","TOTAL_BASES_AFTER_FILTERING",
"GC_CONTENT_AFTER_FILTERING","Q20_RATE_AFTER_FILTERING",
"Q30_RATE_AFTER_FILTERING","DUPLICATION_RATE")
#fastp_process=fastp_process[-1,]
fastp_process=fastp_process[c("SAMPLE",
"TOTAL_READS_BEFORE_FILTERING","TOTAL_BASES_BEFORE_FILTERING",
"GC_CONTENT_BEFORE_FILTERING","Q20_RATE_BEFORE_FILTERING",
"Q30_RATE_BEFORE_FILTERING",
"TOTAL_READS_AFTER_FILTERING","TOTAL_BASES_AFTER_FILTERING",
"GC_CONTENT_AFTER_FILTERING","Q20_RATE_AFTER_FILTERING",
"Q30_RATE_AFTER_FILTERING",
"PASSED_FILTER_READS","CORRECTED_READS","CORRECTED_BASES",
"LOW_QUALITY_READS","TOO_MANY_N_READS","TOO_SHORT_READS","LOW_COMPLEXITY_READS",
"DUPLICATION_RATE")]
fastp_process$TOTAL_READS_BEFORE_FILTERING=fastp_process$TOTAL_READS_BEFORE_FILTERING/1e9
fastp_process$TOTAL_BASES_BEFORE_FILTERING=fastp_process$TOTAL_BASES_BEFORE_FILTERING/1e9
fastp_process$TOTAL_READS_AFTER_FILTERING=fastp_process$TOTAL_READS_AFTER_FILTERING/1e9
fastp_process$TOTAL_BASES_AFTER_FILTERING=fastp_process$TOTAL_BASES_AFTER_FILTERING/1e9
fastp_process$PASSED_FILTER_READS=fastp_process$PASSED_FILTER_READS/100
fastp_process$CORRECTED_READS=fastp_process$CORRECTED_READS/100
fastp_process$LOW_QUALITY_READS=fastp_process$LOW_QUALITY_READS/100
fastp_process$TOO_SHORT_READS=fastp_process$TOO_SHORT_READS/100
SPECIES=c()
LOCATION=c()
inter=c()
for (i in 1:nrow(fastp_process)){
SPECIES[i]=substr(fastp_process[i,1], start = 1, stop = 5)
LOCATION[i]=substr(fastp_process[i,1], start = 6, stop = 7)
inter[i]=as.character(fastp_process$SAMPLE[i])
}
fastp_process=cbind(SPECIES,fastp_process)
fastp_process=cbind(LOCATION,fastp_process)
fastp_process=fastp_process[order(fastp_process$SAMPLE),]
fastp_process$LOCATION=factor(fastp_process$LOCATION)
Num_batch=c(rep(3,20), #Aboye
rep(3,14), #Afall
rep(2,1),rep(3,4),rep(2,15), #Cgale
rep(2,20), #Cjuli
rep(1,20), #Dlabr
rep(2,22), #Dpunt
rep(2,20), #Eecnr
rep(3,20), #Gnige
rep(3,5),rep(2,1),rep(3,3),rep(2,6),rep(3,3),rep(2,12), #Hgutt
rep(2,5),rep(1,2),rep(2,6),rep(1,2),rep(2,5), #Lbude
rep(1,20), #Lmorm
rep(1,20), #Mmerl
rep(1,20), #Msurm
rep(1,20), #Peryt
rep(1,7),rep(2,5),rep(1,10), #Scabr
rep(2,14),rep(3,1),rep(2,5), #Scant
rep(3,5),rep(2,2),rep(3,1),rep(2,1),rep(3,1),rep(2,4),rep(3,1),rep(2,3),rep(3,2), #Scine
rep(1,20), #Spilc
rep(1,14),2,rep(1,5), #Ssard
rep(2,22) #Styph
)
fastp_process$Num_batch=as.factor(Num_batch)
redo=c()
for (i in 1:nrow(fastp_process)){
if (substr(fastp_process[i,3], start = 9, stop = 10)=="B" | substr(fastp_process[i,3], start = 9, stop = 10)=="A"){
redo[i]=18
} else {
redo[i]=19
}
}
fastp_process$redo=as.character(redo)
color=c()
for (i in 1:nrow(fastp_process)){
color[i]=as.character(color_med_atl[which(fastp_process$LOCATION[i]==color_med_atl$Location),2])
}
fastp_process$color=color
for (i in 1:nrow(fastp_process)){
if (substr(fastp_process[i,3], start = 9, stop = 10)=="B"){
fastp_process$SAMPLE[i]=substr(fastp_process[i,3], start = 1, stop = 8)
}
}
fastp_process$SPECIES=factor(fastp_process$SPECIES)
num<-which(substr(fastp_process[,3], start = 9, stop = 10)=="_B" | substr(fastp_process[,3], start = 9, stop = 10)=="_A")
fastp_process=fastp_process[-num,]
for (i in 1:nrow(fastp_process)){
fastp_process$SAMPLE[i]=gsub("_.*","",fastp_process$SAMPLE[i])
}
analogy_legend=c(NA,NA,NA,
"Total reads before filtering ",
"Total bases before filtering (Gb)",
"GC content before filtering (%)",
"Q20 rate before filtering (%)",
"Q30 rate before filtering (%)",
"Total reads after filtering (10⁹)",
"Total bases after filtering (Gb)",
"GC content after filtering (%)",
"Q20 rate after filtering (%)",
"Q30 rate after filtering (%)",
"Passed filter reads (%)",
"Corrected reads (%)",
"Corrected bases (%)",
"Low quality reads (%)",
"Too many N reads (%)",
"Too short reads (%)",
"Low complexity reads (%)",
"Duplication rate (%)")
fastp_plot=data.frame(LOCATION=rep(fastp_process$LOCATION,18),
SPECIES=rep(fastp_process$SPECIES,18),
SAMPLE=rep(fastp_process$SAMPLE,18),
param=rep(NA,nrow(fastp_process)*18),
value=rep(0,nrow(fastp_process)*18))
a=1
for (i in 4:21){
for (j in 1:nrow(fastp_process)){
fastp_plot$param[a]=colnames(fastp_process)[i]
fastp_plot$value[a]=fastp_process[j,i]
a=a+1
}
}
fastp_plot=fastp_plot[is.na(fastp_plot$param)==FALSE,]
labels_species=c()
for (sp in 1:length(levels(fastp_process$SPECIES))){
labels_species=c(labels_species,
paste(levels(fastp_process$SPECIES)[sp]," \n n = ",table(fastp_process$SPECIES)[sp],sep=" "))
}
labels_species=as.vector(labels_species)
fastp_plot$LOCATION=factor(fastp_process$LOCATION,levels=c("Li","Mu","Fa","Ga"))
```
Row {.tabset}
-----------------------------------------------------------------------
### Table {data-height=750}
```{r}
a=0
height=2.5
width=7.5
```
```{r}
datatable(fastp_process,
class = 'cell-border stripe',
rownames = FALSE,
filter = 'top', options = list(
pageLength = 100,scrollY=500,autowidth=T,scrollX=100))
```
### Total after filtering
```{r}
ppp <- ggplot(fastp_plot[fastp_plot$param=="TOTAL_READS_AFTER_FILTERING",], aes(x=SPECIES, y=value)) +
geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
#geom_boxplot(outlier.shape = NA,
# outlier.size = 0.000001,
# alpha=0.5,
# width=0.1,
# show.legend = F)+
geom_point(aes(col=LOCATION,
text=paste("Sample: ",SAMPLE, " \n Total reads:",round(value,3),sep="")),size = 1,
position='jitter',
alpha=0.75)+
#stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
stat_summary(fun=median, geom="point", size=2, color="orange")+
scale_x_discrete(name="Species",
labels=labels_species)+
ylab("Total reads after filtering (10^9 bp)")+
xlab("Species")+
theme_classic()+
scale_colour_manual(name = "",
labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
values = brewer.pal(n = 4, name = "RdBu"))+
theme(legend.position="bottom")
ppp<-ggplotly(ppp,tooltip=c("text")) %>% partial_bundle()
if (PRINT_IMAGE==1){
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<- ppp %>%
layout(
images = list(
list(
source = raster2uri(as.raster(img1)),
x = vv[1], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img2)),
x = vv[2], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img3)),
x = vv[3], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img4)),
x = vv[4], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img5)),
x = vv[5], y = 1,
sizex = size.x, sizey = 0.05
),
list(
source = raster2uri(as.raster(img6)),
x = vv[6], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img7)),
x = vv[7], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img8)),
x = vv[8], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img9)),
x = vv[9], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img10)),
x = vv[10], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img11)),
x = vv[11], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img12)),
x = vv[12], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img13)),
x = vv[13], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img14)),
x = vv[14],y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img15)),
x = vv[15], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img16)),
x = vv[16], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img17)),
x = vv[17], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img18)),
x = vv[18], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img19)),
x = vv[19], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img20)),
x = vv[20], y = 1,
sizex = size.x, sizey = 0.1
)
)
)
}
ppp
```
### Total bases after filtering
```{r}
ppp <- ggplot(fastp_plot[fastp_plot$param=="TOTAL_BASES_AFTER_FILTERING",], aes(x=SPECIES, y=value)) +
geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
#geom_boxplot(outlier.shape = NA,
# outlier.size = 0.000001,
# alpha=0.5,
# width=0.1,
# show.legend = F)+
geom_point(aes(col=LOCATION,
text=paste("Sample: ",SAMPLE, " \n Total bases:",round(value,3),sep="")),size = 1,
position='jitter',
alpha=0.75)+
#stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
stat_summary(fun=median, geom="point", size=2, color="orange")+
scale_x_discrete(name="Species",
labels=labels_species)+
ylab("Total bases after filtering (10^9 bp)")+
xlab("Species")+
theme_classic()+
scale_colour_manual(name = "",
labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
values = brewer.pal(n = 4, name = "RdBu"))+
theme(legend.position="bottom")
ppp<-ggplotly(ppp,tooltip=c("text")) %>% partial_bundle()
if (PRINT_IMAGE==1){
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<- ppp %>%
layout(
images = list(
list(
source = raster2uri(as.raster(img1)),
x = vv[1], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img2)),
x = vv[2], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img3)),
x = vv[3], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img4)),
x = vv[4], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img5)),
x = vv[5], y = 1,
sizex = size.x, sizey = 0.05
),
list(
source = raster2uri(as.raster(img6)),
x = vv[6], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img7)),
x = vv[7], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img8)),
x = vv[8], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img9)),
x = vv[9], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img10)),
x = vv[10], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img11)),
x = vv[11], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img12)),
x = vv[12], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img13)),
x = vv[13], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img14)),
x = vv[14],y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img15)),
x = vv[15], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img16)),
x = vv[16], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img17)),
x = vv[17], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img18)),
x = vv[18], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img19)),
x = vv[19], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img20)),
x = vv[20], y = 1,
sizex = size.x, sizey = 0.1
)
)
)
}
ppp
```
### GC content
```{r}
ppp <- ggplot(fastp_plot[fastp_plot$param=="GC_CONTENT_AFTER_FILTERING",], aes(x=SPECIES, y=value)) +
geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
#geom_boxplot(outlier.shape = NA,
# outlier.size = 0.000001,
# alpha=0.5,
# width=0.1,
# show.legend = F)+
geom_point(aes(col=LOCATION,
text=paste("Sample: ",SAMPLE, " \n GC content:",round(value,3),sep="")),size = 1,
position='jitter',
alpha=0.75)+
#stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
stat_summary(fun=median, geom="point", size=2, color="orange")+
scale_x_discrete(name="Species",
labels=labels_species)+
ylab("GC content (%)")+
xlab("Species")+
theme_classic()+
scale_colour_manual(name = "",
labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
values = brewer.pal(n = 4, name = "RdBu"))+
theme(legend.position="bottom")
ppp<-ggplotly(ppp,tooltip=c("text")) %>% partial_bundle()
if (PRINT_IMAGE==1){
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<- ppp %>%
layout(
images = list(
list(
source = raster2uri(as.raster(img1)),
x = vv[1], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img2)),
x = vv[2], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img3)),
x = vv[3], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img4)),
x = vv[4], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img5)),
x = vv[5], y = 1,
sizex = size.x, sizey = 0.05
),
list(
source = raster2uri(as.raster(img6)),
x = vv[6], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img7)),
x = vv[7], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img8)),
x = vv[8], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img9)),
x = vv[9], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img10)),
x = vv[10], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img11)),
x = vv[11], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img12)),
x = vv[12], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img13)),
x = vv[13], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img14)),
x = vv[14],y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img15)),
x = vv[15], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img16)),
x = vv[16], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img17)),
x = vv[17], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img18)),
x = vv[18], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img19)),
x = vv[19], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img20)),
x = vv[20], y = 1,
sizex = size.x, sizey = 0.1
)
)
)
}
ppp
```
### Q20
```{r}
ppp <- ggplot(fastp_plot[fastp_plot$param=="Q20_RATE_AFTER_FILTERING",], aes(x=SPECIES, y=value)) +
geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
#geom_boxplot(outlier.shape = NA,
# outlier.size = 0.000001,
# alpha=0.5,
# width=0.1,
# show.legend = F)+
geom_point(aes(col=LOCATION,
text=paste("Sample: ",SAMPLE, " \n Q20:",round(value,3),sep="")),size = 1,
position='jitter',
alpha=0.75)+
#stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
stat_summary(fun=median, geom="point", size=2, color="orange")+
scale_x_discrete(name="Species",
labels=labels_species)+
ylab("Q20 (%)")+
xlab("Species")+
theme_classic()+
scale_colour_manual(name = "",
labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
values = brewer.pal(n = 4, name = "RdBu"))+
theme(legend.position="bottom")
ppp<-ggplotly(ppp,tooltip=c("text")) %>% partial_bundle()
if (PRINT_IMAGE==1){
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<- ppp %>%
layout(
images = list(
list(
source = raster2uri(as.raster(img1)),
x = vv[1], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img2)),
x = vv[2], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img3)),
x = vv[3], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img4)),
x = vv[4], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img5)),
x = vv[5], y = 1,
sizex = size.x, sizey = 0.05
),
list(
source = raster2uri(as.raster(img6)),
x = vv[6], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img7)),
x = vv[7], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img8)),
x = vv[8], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img9)),
x = vv[9], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img10)),
x = vv[10], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img11)),
x = vv[11], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img12)),
x = vv[12], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img13)),
x = vv[13], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img14)),
x = vv[14],y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img15)),
x = vv[15], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img16)),
x = vv[16], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img17)),
x = vv[17], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img18)),
x = vv[18], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img19)),
x = vv[19], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img20)),
x = vv[20], y = 1,
sizex = size.x, sizey = 0.1
)
)
)
}
ppp
```
### Q30
```{r}
ppp <- ggplot(fastp_plot[fastp_plot$param=="Q30_RATE_AFTER_FILTERING",], aes(x=SPECIES, y=value)) +
geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
#geom_boxplot(outlier.shape = NA,
# outlier.size = 0.000001,
# alpha=0.5,
# width=0.1,
# show.legend = F)+
geom_point(aes(col=LOCATION,
text=paste("Sample: ",SAMPLE, " \n Q30:",round(value,3),sep="")),size = 1,
position='jitter',
alpha=0.75)+
#stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
stat_summary(fun=median, geom="point", size=2, color="orange")+
scale_x_discrete(name="Species",
labels=labels_species)+
ylab("Q30 (%)")+
xlab("Species")+
theme_classic()+
scale_colour_manual(name = "",
labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
values = brewer.pal(n = 4, name = "RdBu"))+
theme(legend.position="bottom")
ppp<-ggplotly(ppp,tooltip=c("text")) %>% partial_bundle()
if (PRINT_IMAGE==1){
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<- ppp %>%
layout(
images = list(
list(
source = raster2uri(as.raster(img1)),
x = vv[1], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img2)),
x = vv[2], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img3)),
x = vv[3], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img4)),
x = vv[4], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img5)),
x = vv[5], y = 1,
sizex = size.x, sizey = 0.05
),
list(
source = raster2uri(as.raster(img6)),
x = vv[6], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img7)),
x = vv[7], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img8)),
x = vv[8], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img9)),
x = vv[9], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img10)),
x = vv[10], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img11)),
x = vv[11], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img12)),
x = vv[12], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img13)),
x = vv[13], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img14)),
x = vv[14],y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img15)),
x = vv[15], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img16)),
x = vv[16], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img17)),
x = vv[17], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img18)),
x = vv[18], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img19)),
x = vv[19], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img20)),
x = vv[20], y = 1,
sizex = size.x, sizey = 0.1
)
)
)
}
ppp
```
### Passed filter reads
```{r}
ppp <- ggplot(fastp_plot[fastp_plot$param=="PASSED_FILTER_READS",], aes(x=SPECIES, y=value)) +
geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
#geom_boxplot(outlier.shape = NA,
# outlier.size = 0.000001,
# alpha=0.5,
# width=0.1,
# show.legend = F)+
geom_point(aes(col=LOCATION,
text=paste("Sample: ",SAMPLE, " \n Passed filter reads:",round(value,3),sep="")),size = 1,
position='jitter',
alpha=0.75)+
#stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
stat_summary(fun=median, geom="point", size=2, color="orange")+
scale_x_discrete(name="Species",
labels=labels_species)+
ylab("Passed filter reads (%)")+
xlab("Species")+
theme_classic()+
scale_colour_manual(name = "",
labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
values = brewer.pal(n = 4, name = "RdBu"))+
theme(legend.position="bottom")
ppp<-ggplotly(ppp,tooltip=c("text")) %>% partial_bundle()
if (PRINT_IMAGE==1){
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<- ppp %>%
layout(
images = list(
list(
source = raster2uri(as.raster(img1)),
x = vv[1], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img2)),
x = vv[2], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img3)),
x = vv[3], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img4)),
x = vv[4], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img5)),
x = vv[5], y = 1,
sizex = size.x, sizey = 0.05
),
list(
source = raster2uri(as.raster(img6)),
x = vv[6], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img7)),
x = vv[7], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img8)),
x = vv[8], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img9)),
x = vv[9], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img10)),
x = vv[10], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img11)),
x = vv[11], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img12)),
x = vv[12], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img13)),
x = vv[13], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img14)),
x = vv[14],y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img15)),
x = vv[15], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img16)),
x = vv[16], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img17)),
x = vv[17], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img18)),
x = vv[18], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img19)),
x = vv[19], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img20)),
x = vv[20], y = 1,
sizex = size.x, sizey = 0.1
)
)
)
}
ppp
```
### Corrected reads
```{r}
ppp <- ggplot(fastp_plot[fastp_plot$param=="CORRECTED_READS",], aes(x=SPECIES, y=value)) +
geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
#geom_boxplot(outlier.shape = NA,
# outlier.size = 0.000001,
# alpha=0.5,
# width=0.1,
# show.legend = F)+
geom_point(aes(col=LOCATION,
text=paste("Sample: ",SAMPLE, " \n Corrected reads:",round(value,3),sep="")),size = 1,
position='jitter',
alpha=0.75)+
#stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
stat_summary(fun=median, geom="point", size=2, color="orange")+
scale_x_discrete(name="Species",
labels=labels_species)+
ylab("Corrected reads (%)")+
xlab("Species")+
theme_classic()+
scale_colour_manual(name = "",
labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
values = brewer.pal(n = 4, name = "RdBu"))+
theme(legend.position="bottom")
ppp<-ggplotly(ppp,tooltip=c("text")) %>% partial_bundle()
if (PRINT_IMAGE==1){
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<- ppp %>%
layout(
images = list(
list(
source = raster2uri(as.raster(img1)),
x = vv[1], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img2)),
x = vv[2], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img3)),
x = vv[3], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img4)),
x = vv[4], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img5)),
x = vv[5], y = 1,
sizex = size.x, sizey = 0.05
),
list(
source = raster2uri(as.raster(img6)),
x = vv[6], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img7)),
x = vv[7], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img8)),
x = vv[8], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img9)),
x = vv[9], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img10)),
x = vv[10], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img11)),
x = vv[11], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img12)),
x = vv[12], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img13)),
x = vv[13], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img14)),
x = vv[14],y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img15)),
x = vv[15], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img16)),
x = vv[16], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img17)),
x = vv[17], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img18)),
x = vv[18], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img19)),
x = vv[19], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img20)),
x = vv[20], y = 1,
sizex = size.x, sizey = 0.1
)
)
)
}
ppp
```
### Corrected bases
```{r}
ppp <- ggplot(fastp_plot[fastp_plot$param=="CORRECTED_BASES",], aes(x=SPECIES, y=value)) +
geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
#geom_boxplot(outlier.shape = NA,
# outlier.size = 0.000001,
# alpha=0.5,
# width=0.1,
# show.legend = F)+
geom_point(aes(col=LOCATION,
text=paste("Sample: ",SAMPLE, " \n Corrected bases:",round(value,3),sep="")),size = 1,
position='jitter',
alpha=0.75)+
#stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
stat_summary(fun=median, geom="point", size=2, color="orange")+
scale_x_discrete(name="Species",
labels=labels_species)+
ylab("Corrected bases (%)")+
xlab("Species")+
theme_classic()+
scale_colour_manual(name = "",
labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
values = brewer.pal(n = 4, name = "RdBu"))+
theme(legend.position="bottom")
ppp<-ggplotly(ppp,tooltip=c("text")) %>% partial_bundle()
if (PRINT_IMAGE==1){
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<- ppp %>%
layout(
images = list(
list(
source = raster2uri(as.raster(img1)),
x = vv[1], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img2)),
x = vv[2], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img3)),
x = vv[3], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img4)),
x = vv[4], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img5)),
x = vv[5], y = 1,
sizex = size.x, sizey = 0.05
),
list(
source = raster2uri(as.raster(img6)),
x = vv[6], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img7)),
x = vv[7], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img8)),
x = vv[8], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img9)),
x = vv[9], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img10)),
x = vv[10], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img11)),
x = vv[11], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img12)),
x = vv[12], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img13)),
x = vv[13], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img14)),
x = vv[14],y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img15)),
x = vv[15], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img16)),
x = vv[16], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img17)),
x = vv[17], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img18)),
x = vv[18], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img19)),
x = vv[19], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img20)),
x = vv[20], y = 1,
sizex = size.x, sizey = 0.1
)
)
)
}
ppp
```
### Low quality reads
```{r}
ppp <- ggplot(fastp_plot[fastp_plot$param=="LOW_QUALITY_READS",], aes(x=SPECIES, y=value)) +
geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
#geom_boxplot(outlier.shape = NA,
# outlier.size = 0.000001,
# alpha=0.5,
# width=0.1,
# show.legend = F)+
geom_point(aes(col=LOCATION,
text=paste("Sample: ",SAMPLE, " \n Low quality reads:",round(value,3),sep="")),size = 1,
position='jitter',
alpha=0.75)+
#stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
stat_summary(fun=median, geom="point", size=2, color="orange")+
scale_x_discrete(name="Species",
labels=labels_species)+
ylab("Low quality reads (%)")+
xlab("Species")+
theme_classic()+
scale_colour_manual(name = "",
labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
values = brewer.pal(n = 4, name = "RdBu"))+
theme(legend.position="bottom")
ppp<-ggplotly(ppp,tooltip=c("text")) %>% partial_bundle()
if (PRINT_IMAGE==1){
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<- ppp %>%
layout(
images = list(
list(
source = raster2uri(as.raster(img1)),
x = vv[1], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img2)),
x = vv[2], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img3)),
x = vv[3], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img4)),
x = vv[4], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img5)),
x = vv[5], y = 1,
sizex = size.x, sizey = 0.05
),
list(
source = raster2uri(as.raster(img6)),
x = vv[6], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img7)),
x = vv[7], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img8)),
x = vv[8], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img9)),
x = vv[9], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img10)),
x = vv[10], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img11)),
x = vv[11], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img12)),
x = vv[12], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img13)),
x = vv[13], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img14)),
x = vv[14],y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img15)),
x = vv[15], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img16)),
x = vv[16], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img17)),
x = vv[17], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img18)),
x = vv[18], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img19)),
x = vv[19], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img20)),
x = vv[20], y = 1,
sizex = size.x, sizey = 0.1
)
)
)
}
ppp
```
### Too many N reads
```{r}
ppp <- ggplot(fastp_plot[fastp_plot$param=="TOO_MANY_N_READS",], aes(x=SPECIES, y=value)) +
geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
#geom_boxplot(outlier.shape = NA,
# outlier.size = 0.000001,
# alpha=0.5,
# width=0.1,
# show.legend = F)+
geom_point(aes(col=LOCATION,
text=paste("Sample: ",SAMPLE, " \n Too many N reads:",round(value,3),sep="")),size = 1,
position='jitter',
alpha=0.75)+
#stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
stat_summary(fun=median, geom="point", size=2, color="orange")+
scale_x_discrete(name="Species",
labels=labels_species)+
ylab("Too many N reads (%)")+
xlab("Species")+
theme_classic()+
scale_colour_manual(name = "",
labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
values = brewer.pal(n = 4, name = "RdBu"))+
theme(legend.position="bottom")
ppp<-ggplotly(ppp,tooltip=c("text")) %>% partial_bundle()
if (PRINT_IMAGE==1){
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<- ppp %>%
layout(
images = list(
list(
source = raster2uri(as.raster(img1)),
x = vv[1], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img2)),
x = vv[2], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img3)),
x = vv[3], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img4)),
x = vv[4], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img5)),
x = vv[5], y = 1,
sizex = size.x, sizey = 0.05
),
list(
source = raster2uri(as.raster(img6)),
x = vv[6], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img7)),
x = vv[7], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img8)),
x = vv[8], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img9)),
x = vv[9], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img10)),
x = vv[10], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img11)),
x = vv[11], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img12)),
x = vv[12], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img13)),
x = vv[13], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img14)),
x = vv[14],y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img15)),
x = vv[15], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img16)),
x = vv[16], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img17)),
x = vv[17], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img18)),
x = vv[18], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img19)),
x = vv[19], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img20)),
x = vv[20], y = 1,
sizex = size.x, sizey = 0.1
)
)
)
}
ppp
```
### Too short reads
```{r}
ppp <- ggplot(fastp_plot[fastp_plot$param=="TOO_SHORT_READS",], aes(x=SPECIES, y=value)) +
geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
#geom_boxplot(outlier.shape = NA,
# outlier.size = 0.000001,
# alpha=0.5,
# width=0.1,
# show.legend = F)+
geom_point(aes(col=LOCATION,
text=paste("Sample: ",SAMPLE, " \n Too short reads:",round(value,3),sep="")),size = 1,
position='jitter',
alpha=0.75)+
#stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
stat_summary(fun=median, geom="point", size=2, color="orange")+
scale_x_discrete(name="Species",
labels=labels_species)+
ylab("Too short reads (%)")+
xlab("Species")+
theme_classic()+
scale_colour_manual(name = "",
labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
values = brewer.pal(n = 4, name = "RdBu"))+
theme(legend.position="bottom")
ppp<-ggplotly(ppp,tooltip=c("text")) %>% partial_bundle()
if (PRINT_IMAGE==1){
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<- ppp %>%
layout(
images = list(
list(
source = raster2uri(as.raster(img1)),
x = vv[1], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img2)),
x = vv[2], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img3)),
x = vv[3], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img4)),
x = vv[4], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img5)),
x = vv[5], y = 1,
sizex = size.x, sizey = 0.05
),
list(
source = raster2uri(as.raster(img6)),
x = vv[6], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img7)),
x = vv[7], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img8)),
x = vv[8], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img9)),
x = vv[9], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img10)),
x = vv[10], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img11)),
x = vv[11], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img12)),
x = vv[12], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img13)),
x = vv[13], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img14)),
x = vv[14],y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img15)),
x = vv[15], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img16)),
x = vv[16], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img17)),
x = vv[17], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img18)),
x = vv[18], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img19)),
x = vv[19], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img20)),
x = vv[20], y = 1,
sizex = size.x, sizey = 0.1
)
)
)
}
ppp
```
### Low complexity reads
```{r}
ppp <- ggplot(fastp_plot[fastp_plot$param=="LOW_COMPLEXITY_READS",], aes(x=SPECIES, y=value)) +
geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
#geom_boxplot(outlier.shape = NA,
# outlier.size = 0.000001,
# alpha=0.5,
# width=0.1,
# show.legend = F)+
geom_point(aes(col=LOCATION,
text=paste("Sample: ",SAMPLE, " \n Low complexity reads:",round(value,3),sep="")),size = 1,
position='jitter',
alpha=0.75)+
#stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
stat_summary(fun=median, geom="point", size=2, color="orange")+
scale_x_discrete(name="Species",
labels=labels_species)+
ylab("Low complexity reads (%)")+
xlab("Species")+
theme_classic()+
scale_colour_manual(name = "",
labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
values = brewer.pal(n = 4, name = "RdBu"))+
theme(legend.position="bottom")
ppp<-ggplotly(ppp,tooltip=c("text")) %>% partial_bundle()
if (PRINT_IMAGE==1){
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<- ppp %>%
layout(
images = list(
list(
source = raster2uri(as.raster(img1)),
x = vv[1], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img2)),
x = vv[2], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img3)),
x = vv[3], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img4)),
x = vv[4], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img5)),
x = vv[5], y = 1,
sizex = size.x, sizey = 0.05
),
list(
source = raster2uri(as.raster(img6)),
x = vv[6], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img7)),
x = vv[7], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img8)),
x = vv[8], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img9)),
x = vv[9], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img10)),
x = vv[10], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img11)),
x = vv[11], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img12)),
x = vv[12], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img13)),
x = vv[13], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img14)),
x = vv[14],y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img15)),
x = vv[15], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img16)),
x = vv[16], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img17)),
x = vv[17], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img18)),
x = vv[18], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img19)),
x = vv[19], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img20)),
x = vv[20], y = 1,
sizex = size.x, sizey = 0.1
)
)
)
}
ppp
```
### Duplication rate
```{r}
ppp <- ggplot(fastp_plot[fastp_plot$param=="DUPLICATION_RATE",], aes(x=SPECIES, y=value)) +
geom_violin(fill="chartreuse3",col="black",alpha=0.25) +
#geom_boxplot(outlier.shape = NA,
# outlier.size = 0.000001,
# alpha=0.5,
# width=0.1,
# show.legend = F)+
geom_point(aes(col=LOCATION,
text=paste("Sample: ",SAMPLE, " \n Duplication rate:",round(value,3),sep="")),size = 1,
position='jitter',
alpha=0.75)+
#stat_summary(fun.data=data_summary,geom="point", size=2, color="orange")+
stat_summary(fun=median, geom="point", size=2, color="orange")+
scale_x_discrete(name="Species",
labels=labels_species)+
ylab("Duplication rate (%)")+
xlab("Species")+
theme_classic()+
scale_colour_manual(name = "",
labels = c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
values = brewer.pal(n = 4, name = "RdBu"))+
theme(legend.position="bottom")
ppp<-ggplotly(ppp,tooltip=c("text")) %>% partial_bundle()
if (PRINT_IMAGE==1){
img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img2<-readPNG(paste(path,"/figures/fish/","Afall",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
size.x=vv[2]-vv[1]
ppp<- ppp %>%
layout(
images = list(
list(
source = raster2uri(as.raster(img1)),
x = vv[1], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img2)),
x = vv[2], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img3)),
x = vv[3], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img4)),
x = vv[4], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img5)),
x = vv[5], y = 1,
sizex = size.x, sizey = 0.05
),
list(
source = raster2uri(as.raster(img6)),
x = vv[6], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img7)),
x = vv[7], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img8)),
x = vv[8], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img9)),
x = vv[9], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img10)),
x = vv[10], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img11)),
x = vv[11], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img12)),
x = vv[12], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img13)),
x = vv[13], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img14)),
x = vv[14],y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img15)),
x = vv[15], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img16)),
x = vv[16], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img17)),
x = vv[17], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img18)),
x = vv[18], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img19)),
x = vv[19], y = 1,
sizex = size.x, sizey = 0.1
),
list(
source = raster2uri(as.raster(img20)),
x = vv[20], y = 1,
sizex = size.x, sizey = 0.1
)
)
)
}
ppp
```
Packages used {data-icon="fa-map"}
=======================================================================
```{r}
installed.packages()[names(sessionInfo()$otherPkgs), "Version"]
```